Background
To access how many reads are sufficient for confidently call VDJ chain type. I subsampled 0.17, 0.33, 0.50, 0.67, 0.83 and 1 of the total VDJ reads from the VDJ demo data. Then I compared the performance from the following aspects
- Overall summary metrics
- VDJ summary metrics
- Number of molecules for each chain type
- Number of T & B cell with paired chains
- Overlap of VDJ genotype amoung differnt subsample rate
- Gamma delta T cell details
Overall summary metrics
Table
|
|
BCR_reads
|
TCR_reads
|
mRNA_reads
|
BCR_reads_per_cell
|
TCR_reads_per_cell
|
mRNA_reads_per_cell
|
No. Cell
|
|
0.17
|
1820500
|
3122026
|
7795724
|
677.0
|
1161.0
|
2899.1
|
2689
|
|
0.33
|
3536562
|
6065149
|
7795724
|
1352.9
|
2320.3
|
2982.3
|
2614
|
|
0.50
|
5360966
|
9192825
|
7795724
|
2050.9
|
3516.8
|
2982.3
|
2614
|
|
0.67
|
7183869
|
12324310
|
7795724
|
2721.2
|
4668.3
|
2952.9
|
2640
|
|
0.83
|
8899642
|
15268995
|
7795724
|
3437.5
|
5897.6
|
3011.1
|
2589
|
|
1
|
10722634
|
18398174
|
7795724
|
4077.0
|
6995.5
|
2964.2
|
2630
|
VDJ summary metrics
Table
|
|
0.17
|
0.33
|
0.50
|
0.67
|
0.83
|
1
|
|
Reads_Cellular_Aligned_to_VDJ
|
3990815.00
|
7751682.00
|
11748252.00
|
15747435.00
|
19511039.00
|
23508003.00
|
|
Reads_CDR3_Valid_Unfiltered
|
3135000.00
|
6089575.00
|
9229733.00
|
12372514.00
|
15330701.00
|
18472896.00
|
|
Reads_CDR3_Valid_Putative
|
2799438.00
|
5279049.00
|
8035262.00
|
10882897.00
|
13208413.00
|
16154927.00
|
|
Pct_Reads_CDR3_Valid_from_Putative_Cells
|
89.30
|
86.69
|
87.06
|
87.96
|
86.16
|
87.45
|
|
Reads_CDR3_Valid_Putative_Corrected
|
2605679.00
|
4910067.00
|
7475808.00
|
10151168.00
|
12334222.00
|
15074284.00
|
|
Pct_Reads_CDR3_Valid_Corrected_from_Putative_Cells
|
83.12
|
80.63
|
81.00
|
82.05
|
80.45
|
81.60
|
|
Mean_Reads_CDR3_Valid_Corrected_per_Putative_Cell
|
969.01
|
1878.37
|
2859.91
|
3845.14
|
4764.09
|
5731.67
|
|
Molecules_Unfiltered
|
86790.00
|
120888.00
|
152504.00
|
182416.00
|
209337.00
|
237544.00
|
|
Molecules_Corrected_Putative
|
40017.00
|
43808.00
|
47067.00
|
50209.00
|
51506.00
|
53779.00
|
|
Mean_Molecules_Corrected_per_Putative_Cell
|
14.88
|
16.76
|
18.01
|
19.02
|
19.89
|
20.45
|
Number of chain molecules
Table
|
|
0.17
|
0.33
|
0.50
|
0.67
|
0.83
|
1
|
|
BCR_Heavy
|
9651
|
10656
|
11413
|
12305
|
12784
|
13250
|
|
BCR_Kappa
|
8703
|
9622
|
10212
|
10574
|
10867
|
11133
|
|
BCR_Lambda
|
5999
|
6487
|
6844
|
7044
|
7225
|
7381
|
|
TCR_Alpha
|
5877
|
6276
|
6893
|
7537
|
7656
|
8230
|
|
TCR_Beta
|
7989
|
8724
|
9464
|
10353
|
10472
|
11145
|
|
TCR_Delta
|
591
|
652
|
746
|
788
|
825
|
862
|
|
TCR_Gamma
|
1207
|
1391
|
1495
|
1608
|
1677
|
1778
|
Number of T&B cell with paired chains
Table
|
|
0.17
|
0.33
|
0.50
|
0.67
|
0.83
|
1
|
|
T_CD4_memory
|
451
|
409
|
427
|
447
|
424
|
445
|
|
T_CD4_naive
|
273
|
264
|
269
|
283
|
270
|
280
|
|
T_CD8_memory
|
171
|
167
|
167
|
171
|
167
|
169
|
|
T_CD8_naive
|
95
|
92
|
92
|
96
|
94
|
96
|
|
T_gamma_delta
|
52
|
51
|
55
|
52
|
54
|
54
|
|
B
|
232
|
238
|
239
|
240
|
241
|
242
|
Overlap of VDJ genotype
B cell

Gamma Delta T cell

CD4 memory T cell

CD4 naive T cell

CD8 memory T cell

CD8 naive T cell

Gamma delta T cell details
Gamma chain genotype
The cell with any void V/D/J segment will be removed 
Gamma chain genotype 3Dbar

3D movie

Gamma chain genotype Heatmap
Delta chain genotype
The cell with any void V/D/J segment will be removed 
Delta chain genotype dotplot
